Unravelling the binding mode of a methamphetamine aptamer: a spectroscopic and calorimetric investigation

Examining the Relationship between Aptamer Complexity and Molecular Discrimination of a Low-Epitope Target

Aptamers are oligonucleotide-based affinity reagents that are increasingly being used in various applications. Systematic evolution of ligands by exponential enrichment (SELEX) has been widely used to isolate aptamers for small-molecule targets, but it remains challenging to generate aptamers with high affinity and specificity for targets with few functional groups. To address this challenge, we have systematically evaluated strategies for optimizing the isolation of aptamers for (+)-methamphetamine, a target for which previously reported aptamers have weak or no binding affinity. We perform four trials of library-immobilized SELEX against (+)-methamphetamine and demonstrate that N30 libraries do not yield high-quality aptamers. However, by using a more complex N40 library design, stringent counter-SELEX, and fine-tuned selection conditions, we identify aptamers with high affinity for (+)-methamphetamine and better selectivity relative to existing antibodies. Bioinformatic analysis from our selections reveals that high-quality aptamers contain long conserved motifs and are more informationally dense. Finally, we demonstrate that our best aptamer can rapidly detect (+)-methamphetamine at toxicologically relevant concentrations in saliva in a colorimetric dye-displacement assay. The insights provided here demonstrate the challenges in generating high-quality aptamers for low complexity small-molecule targets and will help guide the design of more efficient future selection efforts.

Enzyme-aided amplification strategy for sensitive detection of methamphetamine based on fluorescence aptamer sensor

Methamphetamine (METH) abuse poses a serious risk to human health and social stability. It is critical to develop sensitive and selective methods for detecting METH. Here, we develop a fluorescence aptamer sensor to detect METH based on DNA exonuclease III (Exo III), graphene oxide (GO), and FAM-labeled aptamer. First, the sensor used GO's strong binding capacity to adsorb and quench the fluorescence of the aptamer attached to GO surface. When METH was added to the system, the formation of stable complex for aptamer and METH dissociated from the surface of GO, leading to a fluorescence restoration. Then, the fluorescence signal was further amplified by using Exo III to liberate target METH for cyclic hybridization. And the gel electrophoresis experiment further verified the reliability of this strategy. This aptamer sensor exhibited a low detection limit (0.52 nM) and excellent selectivity under optimal conditions. Notably, this sensor has been successfully validated in the detection of METH in urine and saliva samples, exhibited commendable recovery (94.00-104.65%). Its benefits include facile, sensitive, and rapid. Expected to be used in practical METH detection.

Critical Design Factors for Electrochemical Aptasensors Based on Target-Induced Conformational Changes: The Case of Small-Molecule Targets

Nucleic-acid aptamers consisting in single-stranded DNA oligonucleotides emerged as very promising biorecognition elements for electrochemical biosensors applied in various fields such as medicine, environmental, and food safety. Despite their outstanding features, such as high-binding affinity for a broad range of targets, high stability, low cost and ease of modification, numerous challenges had to be overcome from the aptamer selection process on the design of functioning biosensing devices. Moreover, in the case of small molecules such as metabolites, toxins, drugs, etc., obtaining efficient binding aptamer sequences proved a challenging task given their small molecular surface and limited interactions between their functional groups and aptamer sequences. Thus, establishing consistent evaluation standards for aptamer affinity is crucial for the success of these aptamers in biosensing applications. In this context, this article will give an overview on the thermodynamic and structural aspects of the aptamer-target interaction, its specificity and selectivity, and will also highlight the current methods employed for determining the aptamer-binding affinity and the structural characterization of the aptamer-target complex. The critical aspects regarding the generation of aptamer-modified electrodes suitable for electrochemical sensing, such as appropriate bioreceptor immobilization strategy and experimental conditions which facilitate a convenient anchoring and stability of the aptamer, are also discussed. The review also summarizes some effective small molecule aptasensing platforms from the recent literature.